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Sunday, March 10, 2013

Genetic structure of European Russia


A paper at PLoS One reports on the genetic heterogeneity of Russian populations and the discovery of a "new pole of genetic diversity in Northern Europe":

Several studies examined the fine-scale structure of human genetic variation in Europe. However, the European sets analyzed represent mainly northern, western, central, and southern Europe. Here, we report an analysis of approximately 166,000 single nucleotide polymorphisms in populations from eastern (northeastern) Europe: four Russian populations from European Russia, and three populations from the northernmost Finno-Ugric ethnicities (Veps and two contrast groups of Komi people). These were compared with several reference European samples, including Finns, Estonians, Latvians, Poles, Czechs, Germans, and Italians. The results obtained demonstrated genetic heterogeneity of populations living in the region studied. Russians from the central part of European Russia (Tver, Murom, and Kursk) exhibited similarities with populations from central–eastern Europe, and were distant from Russian sample from the northern Russia (Mezen district, Archangelsk region). Komi samples, especially Izhemski Komi, were significantly different from all other populations studied. These can be considered as a second pole of genetic diversity in northern Europe (in addition to the pole, occupied by Finns), as they had a distinct ancestry component. Russians from Mezen and the Finnic-speaking Veps were positioned between the two poles, but differed from each other in the proportions of Komi and Finnic ancestries. In general, our data provides a more complete genetic map of Europe accounting for the diversity in its most eastern (northeastern) populations.


Figure 1. Geographic locations of the populations analyzed. Key: Komi_Izh – Izhemski Komi, Komi_Pr – Priluzski Komi, Rus_Tv – Russians from Tver, Rus_Ku – Russians from Kursk, Rus_Mu – Russians from Murom, Rus_Me – Russians from Mezen, Finns_He – Finns from Helsinki, Finns_Ku – Finns from Kuusamo, Rus_HGDP – Russians from the Human Genome Diversity Panel.


The distinct genetic character of the Komi and other North Russian populations isn't much of a surprise. These groups come from remote and sparsely populated regions near the Urals and the Arctic, and are thus affected by heavy genetic drift as a result of isolation and endogamy. They also carry higher levels of East Eurasian admixture than other Europeans due to contacts with populations of mostly Siberian origin from east of the Urals.

To explore the potential effect of population demographics on the population structures identified, ROH were compared across populations. ROH may indicate prolonged isolation and a reduced population size [29,35].

...

Regardless of the variations in the analysis, the highest nROH and cROH values were found in Izhemski Komi and in the Finnish sample from Kuusamo. Intermediate estimates were observed in Priluzski Komi, Veps, Finns from Helsinki, and Mezen Russians. Other populations had lower nROH and cROH values. An analysis of LD decay across genomes showed that Izhemski Komi and Finns from Kuusamo also exhibited elevated LD (Figure S6). Concomitantly, Priluzski Komi, Veps, Mezen Russians, and Finns from Helsinki exhibited only slightly elevated LD and were more comparable to the level observed in other European samples, including the remaining Russian samples.


These pronounced effects of genetic drift show up on the ADMIXTURE bar graph below, where the most drifted samples, like the Finns from the Kuusamo isolate, create their own clusters at the higher K (number of ancestral populations assumed). On the other hand, the inflated East Eurasian ancestry among the Komi and North Russians, as well as Veps and Baltic Finns, is most easily seen at K=2. It's represented by the green component which peaks in the Chinese sample.




Note also the extreme behavior of many of the samples on the PCA plot below and the bloated genetic distances between them and others in the Fst table. Again, that's mostly due to genetic drift.





Khrunin AV, Khokhrin DV, Filippova IN, Esko T, Nelis M, et al. (2013) A Genome-Wide Analysis of Populations from European Russia Reveals a New Pole of Genetic Diversity in Northern Europe. PLoS ONE 8(3): e58552. doi:10.1371/journal.pone.0058552


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